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From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jan 09 2007 - 22:15:11 CST
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Dear VMD users,
I'm calculating 2D Mean Squared Displacement(MSD) to get diffusion
coefficient.
The following is my script.
I don't know why I get different results with and without "this line"
in the script.
I think I should have the same results because my selection "sel" is
always a residue of the "low_sel" selection.
Is there anything wrong in my script?
+++++++++++++++++++++++++++++++++++++++++
proc diffu_xy { sel f1 } {
set fout [open $f1 w]
set nf [molinfo top get numframes]
set low_sel [atomselect top "resid 4 to 37"]
for { set i 0 } { $i < $nf } { incr i } {
$low_sel frame $i
$sel frame $i <=== "this line"
set com [measure center $low_sel weight mass]
lappend cxy [vecsub [measure center $sel weight mass] $com]
}
set ds 0.0
puts $fout "0 0.0"
for { set i 1 } { $i < 5000 } { incr i } {
for { set j 0 } { $j < [expr $nf - $i] } { incr j } {
set k [expr $j + $i]
set x [expr [lindex [lindex $cxy $k] 0] - \
[lindex [lindex $cxy $j] 0]]
set y [expr [lindex [lindex $cxy $k] 1] - \
[lindex [lindex $cxy $j] 1]]
set ds [expr $ds + ($x * $x + $y * $y)]
}
puts $fout "$i [expr $ds/($nf-$i)]"
set ds 0.0
}
unset cxy
close $fout
}
mol new ../../noWAT.parm7 type parm7 waitfor all
mol addfile ../unwrap.binpos type binpos waitfor all
set sel [atomselect top "resid 4"]
diffu_xy $sel cen-diff5.dat
set sel [atomselect top "resid 5"]
diffu_xy $sel cen-diff6.dat
.
.
.
+++++++++++++++++++++++++++++++++++++++
-- Best wishes, MYUNGGI YI
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